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‎.Rbuildignore‎

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^cran-comments\.md$
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^LICENSE\.md$
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^design$
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^pkgdown$

‎.github/.gitignore‎

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*.html

‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: R-CMD-check
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (R ${{ matrix.config.r }})
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: macos-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/lint.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: lint
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name: lint.yaml
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permissions: read-all
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jobs:
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lint:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::lintr, any::styler
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extra-packages: any::lintr, local::.
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needs: lint
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- name: Lint
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run: lintr::lint_package()
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shell: Rscript {0}
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- name: Style check
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run: styler::style_pkg(dry = "fail")
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shell: Rscript {0}
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env:
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LINTR_ERROR_ON_LINT: true

‎.github/workflows/pkgdown.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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name: pkgdown.yaml
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permissions: read-all
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name }}
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4
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uses: JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean: false
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branch: gh-pages

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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name: test-coverage
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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covr::codecov(
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \;
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results

‎.gitignore‎

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# devtools
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/doc/
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/Meta/
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docs

‎DESCRIPTION‎

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LazyDataCompression: xz
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Encoding: UTF-8
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Config/testthat/edition: 3
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URL: https://github.com/humanpred/cdiscdata
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URL: https://github.com/humanpred/cdiscdata, https://humanpred.github.io/cdiscdata/
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BugReports: https://github.com/humanpred/cdiscdata/issues
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VignetteBuilder: knitr
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RoxygenNote: 7.3.3

‎README.md‎

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# cdiscdata
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<!-- badges: start -->
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[![R-CMD-check](https://github.com/humanpred/cdiscdata/actions/workflows/R-CMD-check.yaml/badge.svghttps://github.com/humanpred/cdiscdata/actions/workflows/R-CMD-check.yaml/badge.svghttps://github.com/humanpred/cdiscdata/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/humanpred/cdiscdata/actions/workflows/R-CMD-check.yaml)
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[![Codecov test coverage](https://codecov.io/gh/humanpred/cdiscdata/graph/badge.svg)](https://app.codecov.io/gh/humanpred/cdiscdata)
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<!-- badges: end -->
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`cdiscdata` provides versioned CDISC Controlled Terminology (SDTM, ADaM)
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and Define-XML schemas (XSD) and CDISC XSLT stylesheets. Uses a
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validity-date design to store all historical CT versions compactly
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without redundant row duplication. Intended as a shared data
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dependency for pharmaverse-aligned packages.
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## Installation
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You can install the development version of cdiscdata from [GitHub](https://github.com/) with:
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``` r
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# install.packages("pak")
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pak::pak("humanpred/cdiscdata")
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```
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## Example
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This is a basic example which shows you how to solve a common problem:
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``` r
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library(cdiscdata)
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## basic example code
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```

‎_pkgdown.yml‎

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url: https://humanpred.github.io/cdiscdata/
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template:
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bootstrap: 5
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navbar:
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structure:
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left: [intro, reference, articles, news]
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reference:
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- title: "Data catalogue"
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contents:
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- list_datasets
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- cdiscdata_versions
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- title: "Version discovery"
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contents:
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- available_ct_versions
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- title: "Data retrieval"
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contents:
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- get_dataset
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- get_ct
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- title: "File paths"
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contents:
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- schema_path
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- stylesheet_path
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- title: "Datasets"
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contents:
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- ct_sdtm
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- ct_adam
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- datasets_catalogue
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articles:
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- title: "Guides"
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navbar: ~
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contents:
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- cdiscdata
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- versioning

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